diff --git a/crates/codegraph-cli/tests/full_sync_scope.rs b/crates/codegraph-cli/tests/full_sync_scope.rs
new file mode 100644
index 00000000..e664945a
--- /dev/null
+++ b/crates/codegraph-cli/tests/full_sync_scope.rs
@@ -0,0 +1,122 @@
+//! A full `sync` keeps exactly the files `index` keeps.
+//!
+//! The watcher deliberately prunes some directories the scan indexes: the
+//! watch-only defaults such as `.cache`, and every top-level `.codegraph-*`
+//! directory. A full sync used to judge scope with that stricter watch policy,
+//! so `sync` deleted files `index` had just indexed, and `status` then reported
+//! them as pending additions — `sync` no longer equalled `index --force`.
+
+use std::fs;
+use std::path::{Path, PathBuf};
+use std::process::Command;
+
+struct TestDir {
+    path: PathBuf,
+}
+
+impl TestDir {
+    fn new(label: &str) -> Self {
+        let path = std::env::temp_dir().join(format!(
+            "codegraph-cli-full-sync-scope-{label}-{}-{}",
+            std::process::id(),
+            std::time::SystemTime::now()
+                .duration_since(std::time::UNIX_EPOCH)
+                .unwrap()
+                .as_nanos()
+        ));
+        fs::create_dir_all(&path).unwrap();
+        Self { path }
+    }
+}
+
+impl Drop for TestDir {
+    fn drop(&mut self) {
+        let _ = fs::remove_dir_all(&self.path);
+    }
+}
+
+fn cli(args: &[&str]) -> String {
+    let output = Command::new(env!("CARGO_BIN_EXE_codegraph"))
+        .args(args)
+        .env("CODEGRAPH_NO_DAEMON", "1")
+        .output()
+        .expect("run codegraph binary");
+    assert!(
+        output.status.success(),
+        "codegraph {args:?} failed: stdout={} stderr={}",
+        String::from_utf8_lossy(&output.stdout),
+        String::from_utf8_lossy(&output.stderr)
+    );
+    String::from_utf8_lossy(&output.stdout).into_owned()
+}
+
+fn touch(root: &Path, relative: &str, contents: &str) {
+    let path = root.join(relative);
+    fs::create_dir_all(path.parent().unwrap()).unwrap();
+    fs::write(path, contents).unwrap();
+}
+
+fn indexed_paths(project: &str) -> Vec<String> {
+    let value: serde_json::Value =
+        serde_json::from_str(&cli(&["files", "-p", project, "--json"])).expect("files JSON");
+    let mut paths: Vec<String> = value
+        .as_array()
+        .expect("files array")
+        .iter()
+        .map(|file| file["path"].as_str().expect("path").to_string())
+        .collect();
+    paths.sort();
+    paths
+}
+
+fn pending_total(project: &str) -> u64 {
+    let value: serde_json::Value =
+        serde_json::from_str(&cli(&["status", project, "--json"])).expect("status JSON");
+    let pending = &value["pendingChanges"];
+    ["added", "modified", "removed"]
+        .iter()
+        .map(|key| pending[*key].as_u64().expect("pending count"))
+        .sum()
+}
+
+#[test]
+fn full_sync_keeps_files_the_watcher_does_not_watch() {
+    let dir = TestDir::new("watch-only");
+    let project = dir.path.join("proj");
+    touch(&project, "src/app.ts", "export const app = 1;\n");
+    // `.cache` and `vcpkg_installed` are watch-only ignores; the scan indexes
+    // them. A top-level `.codegraph-*` directory that is not the index root is
+    // scanned too, but the watcher rejects it.
+    touch(&project, ".cache/cached.ts", "export const cached = 1;\n");
+    touch(
+        &project,
+        "vcpkg_installed/port.ts",
+        "export const port = 1;\n",
+    );
+    touch(
+        &project,
+        ".codegraph-sources/kept.ts",
+        "export const kept = 1;\n",
+    );
+    let p = project.to_str().unwrap();
+
+    cli(&["init", p]);
+    let indexed = indexed_paths(p);
+    assert_eq!(
+        indexed,
+        vec![
+            ".cache/cached.ts".to_string(),
+            ".codegraph-sources/kept.ts".to_string(),
+            "src/app.ts".to_string(),
+            "vcpkg_installed/port.ts".to_string(),
+        ]
+    );
+    assert_eq!(pending_total(p), 0, "a fresh index has nothing pending");
+
+    cli(&["sync", p]);
+    assert_eq!(indexed_paths(p), indexed, "sync must keep what index keeps");
+    assert_eq!(pending_total(p), 0, "status must agree with sync");
+
+    cli(&["index", "--force", p]);
+    assert_eq!(indexed_paths(p), indexed, "sync equals index --force");
+}
diff --git a/crates/codegraph-watch/src/sync.rs b/crates/codegraph-watch/src/sync.rs
index 780b9b13..5b06fbb8 100644
--- a/crates/codegraph-watch/src/sync.rs
+++ b/crates/codegraph-watch/src/sync.rs
@@ -269,6 +269,7 @@ fn sync_project_once_with_scope(
                 &mut store,
                 project_root,
                 candidates,
+                Some(&on_disk),
                 scope,
                 &include,
                 &exclude,
@@ -423,6 +424,7 @@ fn sync_changed_paths_current_scope(
                 &mut store,
                 project_root,
                 changed,
+                None,
                 &scope,
                 &include,
                 &exclude,
@@ -448,6 +450,7 @@ fn sync_paths_with_store(
     store: &mut Store,
     project_root: &Path,
     paths: impl IntoIterator<Item = impl AsRef<Path>>,
+    scanned: Option<&HashSet<String>>,
     scope: &ProjectScope,
     include: &[String],
     exclude: &[String],
@@ -484,7 +487,15 @@ fn sync_paths_with_store(
             continue;
         }
         outcome.files_checked += 1;
-        let in_scope = policy.should_handle_file(&relative);
+        // A full sync reconciles against the scan it just ran, so the scan alone
+        // decides scope, exactly as for `index --force`. The watch policy is
+        // stricter on purpose (it never watches `.cache`, a top-level
+        // `.codegraph-*` directory, and the other watch-only defaults), so it may
+        // only judge the paths an incremental sync was handed.
+        let in_scope = match scanned {
+            Some(scanned) => scanned.contains(&relative),
+            None => policy.should_handle_file(&relative),
+        };
         if !in_scope && store.file_by_path(&relative)?.is_none() {
             outcome.files_ignored += 1;
             on_progress(done + 1, total);